Journal of Survey in Fisheries Sciences 4(1) 54-93 2017

A Review of Fish Taxonomy Conventions and Species

Identification Techniques

Keat-Chuan Ng C.1; Aun-Chuan Ooi P.

1; Wong W.L.

1; Khoo G.

1*

Received: December 2016 Accepted: March 2017

Abstract

Taxonomists, ecologists, geneticists or researchers from other biological fields who

wish to adopt fish as a constituent of their studies often become discouraged when they

find that ichthyology is a complex subject. In fish-based studies, the failure to recognize

fishes as distinct biological units can lead to wrong diagnosis. Hence, this review paper

attempts to clarify and discuss the latest schools of thought pertaining to fish taxonomy

and the techniques for species identification. It is hoped that the contents and

illustrations in this paper will assist researchers in laying a good foundation to inform

their studies.

Keywords: Fish, Morphology, Molecular, Taxonomy, Species identification

1-Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat,

31900 Kampar, Perak, Malaysia.

*Corresponding author's Email: gideonkhoo@utar.edu.my

55 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Introduction

The term “fish” is usually a convenient

description for a group of poikilothermic

(cold-blooded) aquatic vertebrates under

the Chordata phylum that breathe with

gills (Nelson, 2006). Scientifically, the

collective term of “fish” primarily refers

to Agnatha (jawless fishes),

Chondrichthyes (sharks and rays),

Sarcopterygii (lobe-finned fishes), and

Actinopterygii (ray-finned fishes).

Actinopterygians, the bony or ray-finned

fishes, are without a doubt the majority of

fishes found in freshwaters.

Actinopterygians have lepidotrichia which

are characterized by fins of membranous

webs held together by bony spines, or

rays. This niche character differentiates

Actinopterygians from Sarcopterygians

which possess lepidotrichia that are

fleshy.

Although in early 20th century, the

ichthyologist Regan (1910) defined a fish

species as a product of interrelated

communities with common morphological

features (today this is termed as

“morphospecies”), it should be noted that

the species classification concept differs

among scientists. While authorities such

as Nelson (2006) and Mayr (1942) accept

the “biological species” concept, others

like Simpson (1951) promotes the

“evolutionary species” concept. Then

there is Cracraft (1983) who prefers to

adopt the “phylogenetic” or “cladistic”

species concept.

The oldest and most widely practised

“biological species” concept postulates

that species are part of a group

composition that breed or can potentially

interbreed in natural conditions. In the

“evolutionary species” concept, a species

is a representative of a lineage having its

own evolutionary affinity and historical

destiny. As for the “phylogenetic species”

concept, species is viewed as a

monophyletic set of organism with

common ancestors. In practice, each of

these major concepts is prone to some

level of subjectivity. Regardless of

concept, wildlife scientists, especially

ichthyologists, typically identify and

name fishes by either by their consistency

in morphological, and more recently,

molecular characteristics.

While most researchers are concerned

with fishes as a food source and their

work involves enriching the body of

aquaculture knowledge, there are some

who are interested in their diversity,

distribution patterns, ecology and

functional physiology. Recently, there has

also been an overwhelming interest in the

molecular constitution of fishes (Wong et

al., 2011; Pereira et al., 2013; Rakshit et

al., 2015 Quraishia et al., 2015) and their

function as biological indicators to

monitor waterbody pollution (Fonge et

al., 2011; Khodadoust et al., 2013;

Authman et al., 2015). Correspondingly,

the interest in fish has expanded

exponentially, and the ichthyology

discipline is often sought to contribute too

many other fields of studies (Padilla and

Williams, 2004; Lauder et al., 2007; Feist

and Longshaw, 2008; Rudkowska et al.,

2010). Generally, species is the basic unit

in these studies and sound taxonomy is a

prerequisite to prevent confusion and

misinterpretation.

Journal of Survey in Fisheries Sciences 4(1) 2017 56

However, researchers who wish to

adopt fish as a major or minor component

of their studies will be discouraged when

they discover that ichthyology is not an

easy subject, more so fish taxonomy.

Also, it is a common knowledge that there

is already an acute shortage of fish

taxonomists and finding a fish taxonomist

to assist in a study is often difficult. Such

is the same case with many other taxa.

Since fish diversity can be high,

especially in tropical countries, a

taxonomist is typically overwhelmed with

constant scientific name revisions, field

collection expeditions and managing a

museum. Moreover, taxonomy cannot be

commercialized and it sees very little

funding in many countries. Thus, the

discipline rarely attracts students or can

sustain career taxonomists in the

universities. Such a problem has caused

taxonomic errors in published papers and

the condition is now widely known as the

“taxonomy impediment” (Wheeler et al.,

2004; de Carvalho et al., 2007). It is often

said that the discipline of taxonomy

would be extinct earlier than most

endangered species.

On hindsight, the advancement of

molecular, computerized and statistical

techniques have led many to believe that

“species” can be easily characterized by

nucleotide sequences, software and

mathematical calculations, and the

knowledge in taxonomy is no longer

needed. Ebach and Holdrege (2005) warn

us that there are a growing number of

researchers who have never wet their feet

in the rivers to observe species or build

competency in applying nomenclature

rules, and yet set out to conduct fish-

based studies and publish papers. Since

they lack field experiences, many are

unaware of distinctive fish characteristics

such as phenotypic polymorphisms,

sexual dimorphism and behavioural

divergence due to the regional speciation

process (Waugh, 2007). Failing to

recognize such exceptions can lead to

wrong species diagnosis. Some

researchers restrict themselves to

laboratories, ornamental fish and

aquaculture farms, and their specimens

may look very different from the wild

type which the scientific name was

derived from. Ideally, it is advisable to

treat a selective bred variety raised in

artificial conditions differently.

Otherwise, publication with nomenclature

errors will be perpetuated through citation

and cause a chaotic situation.

In lieu of concerns highlighted, this

review attempts to provide a concise

introduction to this complex but important

field. To understand fish as a biological

unit, the readers should also have some

background in zoology. Our objective is

not to polarize techniques for fish

identification because we are convinced

that each technique has its merits. Their

shortcomings will, however, be discussed

to assist researchers in making sound

judgments and decisions.

This paper reviews and discusses

taxonomic concerns of freshwater species

that belong to the Actinopterygii class,

and we assume that readers have some

familiarity with ray-finned fish anatomy

and the common species. Given that a

picture is worth a thousand words, we

57 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

believe that taxonomy can be easier to

master if the reader is provided with

detailed scientific illustrations and colour

images. This review is by no means

comprehensive but we hope it will set a

good foundation for those who wish to

make a competent start in species-level

research.

Why are there do many species?

Teleost species form the largest category

among vertebrate animals and their

numbers have reached more than 32,500

valid marine and freshwater species under

515 families (Nelson, 2006). In the global

context, there are roughly 11,952 of

freshwater species (Helfman et al., 2009).

Ricklefs (2004) suggests that competition

and mutualism among species have an

effect on species abundance while Wright

et al. (2003) speculate that species

diversity is the result of productivity from

available “energy” in a particular region.

If a region lacks energy (e.g., low food

availability in the desert), species richness

is typically low. However, in the case of

fish, MacArthur’s (1969) hypothesis

seems to be the most probable as he

suggests that species diversity is

accelerated if there are more areas to host

suitable habitats. The hypothesis

corresponds with the reality today as large

freshwater regions seem to demonstrate

more genera and species, for example the

Neotropical region (705 genera, 4,035

species) compared to the Australian

region (94 genera, 261 species) (Leveque

et al., 2008) (Fig. 1).

Early taxonomists, namely Linnaeus

and Darwin, had started cataloguing and

clustering species that looked similar

because they believed that these species

share a common biological lineage. In the

mid-18th

century, the evolution hypothesis

was a new and strange concept.

Eventually this was proven to be factual

in the advent of modern molecular and

genetic assessment technologies. In

general, today, there is a consensus

among scientists that all species on Earth

are interlinked with a hierarchical and

evolutionary tree with millions of

branches. Each branch itself is a

representation of the natural history of a

particular species and its pedigree. But

why did the branches have to extend and

multiply in the first place? What causes

the divergence?

When gene flow among populations is

interrupted by natural (e.g., geographic

barriers created by earthquakes) or

artificial means (e.g., man-made barriers

in aquaculture farms and dams), two types

of speciation will occur, namely allopatric

speciation and sympatric speciation

(Butlin et al., 2016) (Fig. 2). Allopatric

speciation occurs when a population is

separated by a barrier and such isolation

prevents the two or more sub-populations

from mating. Given time, the lack of gene

flow among the sub-populations will

cause biological incompatibility and

divergence would be triggered (Mayr,

1959; Turelli et al., 2001; Singh 2012).

Journal of Survey in Fisheries Sciences 4(1) 2017 58

Figure 1: Major freshwater fish Eco regions encompassing 1,054 rivers as classified by the Fish-

SPRICH database (Source: Brosse et al., 2012).

Figure 2: Modes of speciation.

In sympatric speciation, biologists

highlight that ecological shift and

resource competition are the key drivers

(Mayr, 1947; Dieckmann and Doebeli,

1999; Bolnick and Fitzpatrick, 2007;

Mallet et al., 2009). They reasoned that

new species may arise within a population

from biological reproductive barriers

between mutants that are better adapted

and parent populations. Nonetheless,

despite further speciation in both space

and time, and regardless of allopatric or

sympatric speciation, species within a

branch would still maintain a certain

degree of morphological similarity (Butlin

et al., 2016).

Taxonomy and systematics

The word taxonomy originated for Greek

word taxis, meaning arrangement, and

nomos, meaning law. The science of

biological taxonomy is responsible for

discovering, describing, classifying,

naming and treating each species as the

basic unit. Species are given names in

accordance to the protocol set by

59 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Linnaeus’ binomial nomenclature system

(Enghoff, 2009). Systematics on the other

hand is the science of distinguishing

orderliness and classification of a taxon

into hierarchical series to emphasize their

interrelationships (Mayr, 1942; Guerra-

Gracia et al., 2008). The word

systematics stems from Greek word

systema. Nelson (2006) tells us that a

systematist seeks the broadest outlook to

resolve family, relative, order or grouping

orderliness. Taxonomy and systematics

are not entirely different schools of

thought, but rather overlapping fields

(Wilson, 1985; Lincoln et al., 1998).

Kapoor (1998) and Wägele (2005) also

highlight that the term “systematics” is

often used synonymously with taxonomy.

It must be clarified that this review adopts

Nelson’s (2006) argument that biological

classification is based on systematic

studies and taxonomy is part of

systematics.

A proper taxonomy is a first-hand and

exhaustive undertaking. Whether one

adopts the “biological species” concept

(Mayr, 1942; Nelson, 2006),

“evolutionary species” concept (Simpson,

1951) or the “phylogenetic species”

concept (Cracraft, 1983) as explained

earlier, all identification processes start

which examining morphotypes at the

earliest stage of discovery. Specimens are

physically scrutinized from small

microscopic configuration of scales to

large membrane patterns of the caudal fin.

Each physical variance, no matter how

small, on a fish body is useful

information. Naturally, all fish-based

studies require considerable identification

skills, experiences and familiarity with

local species. Nonetheless, this may not

be as complex as it sounds because each

species is normally distinctive in

appearance and has a certain “look” (Fig.

3).

At a higher level and broader

perspective, systematists are experts who

examine historical discrepancies,

ambiguities, errors and variant names of

species, genus and family. For example,

there is the problem with regards to

whether Eleotridae or Eleotrididae should

be used for the members of sleeper fishes

(Robins, 1991). Thankfully, species

classification and naming consistency is

slowly being resolved and currently

governed by the International

Commission on Zoological Nomenclature

(ICZN). However, fish taxonomic

problems cannot be resolved quickly as

desired because ICZN also has to address

issues affecting other taxa. For the fish

taxon, appreciatively, there are dedicated

ichthyologists who take it upon

themselves to diligently keep track of the

latest development and progressively

publish the most updated information.

Every species belongs to a genus

(plural: genera), every genus to a family,

every family to an order, every order to a

class, every class to a phylum (plural:

phyla) and finally all phyla are placed

under an overarching kingdom (Fig. 4).

Each phylum is regarded as a

representation of a large grouping of

species that shares a common ancestor in

evolution.

Journal of Survey in Fisheries Sciences 4(1) 2017 60

Figure 3: Species from each family have a similar morphological profile to provide identification

clues (Source: Adapted from Rainboth, 1996).

Figure 4: Taxonomic ranking and naming convention.

Ray-finned fish which is reviewed in this

paper belongs to the Actinopterygii class

under the Chordata phylum in the

Animalia kingdom. Such is the ranking

and principle of taxonomy practice used

to organize all biological units. At time of

writing, some experts have arrived at

some agreement and the “Family-group

Names of Recent Fishes” published by

Van der Laan et al. (2014) seems to be the

most updated for family naming.

In fish taxonomy, there are established

conventions for expressing taxonomic

ranking. According to ICZN regulation,

the family-group name must always end

with the “idae” suffix (e.g., Cyprinidae)

and the subfamily-group name must end

with the “inae” suffix (e.g., Cyprininae).

At a higher level, the order-group name

should end with the “iformes” suffix (e.g.,

Cypriniformes) and the suborder-group

name must end with the “oidea” suffix

(e.g., Cyprinioidea). The family names are

always capitalized but never italicized.

61 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

How species are named and why

In Latin, species means “a kind,

appearance and quality”. Depending on

locality, people have various vernacular

and common names for a fish species. For

example, the common names Pearl

Gourami, Diamond Gourami and Mosaic

Gourami all refer to the same species.

Therefore, the use of common names can

be confusing and misleading. However,

its scientific name Trichogaster leeri is a

unique name and there is no chance that

the name may be mistaken with other

species. Ideally, a scientific name may

even tell something about the species' key

characteristics (Fig. 5), its habit,

discoverer and perhaps the location where

it was first found.

Figure 5: The species name Leptobarbus rubripinna is derived from Greek word “leptós” which

means thin or slender, and the Latin word “barbus” meaning barbel. Rubripinna

originates from the Latin words “ruber” and “pinna” which mean red and fin,

respectively.

Another interesting example is the

fighting fish species, Betta persephone,

which is named after Persephone the

daughter of Zeus in Greek mythology.

Also known as the princess of darkness

because she is said to rule the underworld,

Persephone was the perfect epithet for B.

persephone which typically inhabits the

black water in peat-swamp habitats of

Southeast Asia. Another fighting fish

species the Betta gladiator need no

further explanation as to why the epithet

was given.

The Kottelatia genus (with only one

recognized cyprinid species, Kottelatia

brittani) was named after a prominent

ichthyologist Maurice Kottelat, and a

species that is named Anguilla borneensis

tells us that it was first described from

specimens found in Borneo island. Those

familiar with Latin or Greek, the

traditional language used in scientific

names, would also be able to tell that the

catfish Clarias leiacanthus should have

pectoral spines with smooth anterior edge;

in Greek, “leios” means smooth and

“akathos” means thorn. The Bihunichthys

monopteroides was named after a popular

food in Southeast Asia; “bihun” is a local

name for rice noodle and “ichtys” means

Journal of Survey in Fisheries Sciences 4(1) 2017 62

fish in Greek. Sure enough, it is a very

small and thin spineless eel that resembles

rice noodles. From examples mentioned, a

scientific name can be communicative and

gives species stable and universal

designations for easy retrieval.

The scientific naming that we practice

today would not be possible without the

foundation laid by Carl Linnaeus (1707-

1778). Often confused by the many

dialectal names during his specimen

collection work in various countries,

Linnaeus was convinced that species

names must be standardized. In 1735, he

published a small pamphlet titled Systema

Naturae (The System of Nature) to

introduce his new system of giving and

organizing species names. Linnaeus also

decided that species names should be

given in Latin or Greek in two parts. Thus

the binomial nomenclature system was

conceived. Although the Systema

Naturae was meant for naming plants, it

soon gained popularity due to its

practicality and it was quickly adopted by

taxonomists of various taxa.

The rule of binomial nomenclature

dictates that the first part of species name

comprises of its genus (noun) and it is

always capitalized (e.g., Cyprinus). The

second part is used to describe the

species’ attribute or epithet (adjective)

and it is never capitalized (e.g., Cyprinus

hyperdorsalis; “hyper” meaning “over” in

Greek and “dorsalis” meaning the back

part of the body in Latin). The first and

second part is always italicized. However,

if the neighbouring texts are italicized,

then the first and second name would be

non-italicized (e.g., in mesohabitat that

hosts an isolated Channa gachua

population …). This is to ensure that the

species name is outstanding and can be

easily singled out during reading. When

handwritten, species name should be

underlined for the same reason. The first

part may be used alone but the second

part is never used by itself.

A species name must be written in full

the first time is it expressed in a

manuscript (e.g., Cyprinus hyperdorsalis)

and thereafter the first part, or genus

name, can be abbreviated with initial

capital letter (e.g., C. hyperdorsalis) on

the condition that there is no

misconstruing with other genera (i.e.,

bearing in mind “C. can also mean

Channa or Clarias if these genera appear

on the same paper). In cases where an

abbreviated initial capital letter may cause

confusion, two letters may be used (e.g.,

Ch. for Channa or Cl. for Clarias). There

is no absolute rule and the objective is to

avoid misinterpretation.

Additionally, “sp.” (Singular) or “spp.”

(Plural) may be used to represent

“species” to indicate partially identified

species with the genus known. For

example, when a specimen is recorded as

Cyprinus sp. it denotes that a specimen of

the Cyprinus genus cannot be identified to

species level, possibly due to it being a

small juvenile which makes positive

identification difficult. For species with

problematic identification, it may also be

recorded with the term “cf.” added

between the scientific names. It is simply

a short term for “confer” or “compare

with”. For example, when a species is

referred as Rasbora cf. elegans, it implies

63 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

the species it most likely belongs to but

the designation is still marred by

unresolved taxonomic issues or more

work is needed to be completely sure.

Alternatively, the term “aff.” is sometimes

added between the scientific name when a

specimen cannot be matched to any

species known to science, or it is a new

species that is yet to be named. The term

is a short form of “affinis” in Latin which

means “akin to”. The insertion of “aff.” is

to associate the possibility of a new

species with the closest species (e.g.,

Rasbora aff. elegans).

It would be advisable to describe the

genus, species, author and year in full

when a species name is expressed as part

of a manuscript title, or the first time it is

written in the manuscript. The author(s)’

name(s) who first coined the binomial

name and year of publication should be

included (e.g., Cyprinus hyperdorsalis

Nguyen, 1991) because it is a good

practice to ensure the manuscript author is

explicitly referring to a species described

by a particular taxonomist in a particular

year. The author’s name is typically

enclosed in parentheses when the genus is

no longer the original one used.

Alternatively, the author’s name is

enclosed within parenthesis when a

species has been transferred from the

original genus in which it was first

described; e.g. Cyprinus melanes (Mai,

1978). This puts the author and the reader

in a safer position because literature that

adopts fish as a subject can be flawed by

synonyms and obsolete species’ names. It

should be noted that the author citation is

treated differently in various taxa. Also,

when submitting a manuscript for peer

review, it would be wise to countercheck

the journal's submission instructions on

how to quote the target species.

Species identification at the

morphological level

Since humans learnt how to hunt fish,

species were identified based on some

simple anatomical features. Observation

of specimen anatomy and differentiating

fish species based on their morphological

features is the most practical, rapid and

low cost method. Besides experienced

local fisherman and fish mongers, people

who live by the river or wetland would

learn to identify fishes at a young age.

This is due to knowledge and memory

acquired from long-term observation or

through oral tradition maintained by

elders. Such traditional knowledge has

been interweaved into modern

ichthyology by many researchers

(Calamia, 1999; Drew, 2005; Stacey et

al., 2008; MacLean et al., 2009; Ferreira

et al., 2014), and the term for it is

“traditional ecological knowledge” (TEK)

(Berkes et al., 2000). For those keen in

taxonomy, however, there is a need to

adopt a more precise and sound approach.

Fish identification is the most

important component in any fish-based

study and acquiring reasonable

competency always begins with the study

of fish anatomy. Fundamentally, fish

species have to “go with the flow”. It is

apparent that the anatomy of fish is

shaped by the physical properties of

water, the essential liquefied medium in

which the fish adopts as habitat. Water is

Journal of Survey in Fisheries Sciences 4(1) 2017 64

dense but holds relatively small amounts

of oxygen which affects fish respiratory

function. Water also absorbs light in

higher intensity than air which affects fish

visual capacity. Water can flow fast or not

at all, and this affects how fishes

manoeuvre in water. Such a complex and

fluid environment calls for special

adaptations to live in and fishes have

evolved precisely to fit in.

In general, most biological adaptations

in fish occur in the body, mouth, fins, skin

coloration and reproductive traits. The

body of a bony ray-finned fish comprises

3 sections; the head, trunk and caudal or

tail. The head is a region from the mouth

tip to the posterior edge of the gill cover.

The trunk contains the abdominal cavity

and it forms the main body that lies

between the head and caudal (Fig. 6). In

most species, the trunk is narrowed down

at an area called the caudal peduncle

where it is connected to the caudal fin,

which is a prominent feature on the body

of a fish.

Body flexure attained by contractions

of the myomeres and thrust from fins is

responsible for fish propulsion. Fin shapes

and sizes vary tremendously and they are

used for stabilizing, reversing, stopping,

descending, ascending and manoeuvring.

In morphometric (Figs. 7 and 8) and

meristic identification of fishes, the

positions of fins, numbers and types of

ray or spine composition are useful (Figs.

9, 10 and 11).

Figure 6: An example of key morphological features of a species from the Cyprinidae family

(Source: Adapted from Rainboth, 1996).

Figure 7: Common morphometric data collected for fish identification (Source: Adapted from

Rainboth, 1996).

65 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Figure 8: Common measurements between key points to construct patterns that quantify

morphometric variance between species (Source: Adapted from Strauss and Bookstein,

1982).

Figure 9: A close-up view of fin rays which epitomises fish under the Actinopterygii class.

Journal of Survey in Fisheries Sciences 4(1) 2017 66

Figure 10: An example of fin positions and ray structures of a fish with a contiguous dorsal fin.

Figure 11: A specimen from the Gastromyzon genus with specialized suctorial pectoral fins and

fused pelvic fins for adhering to substratum rocks in riffles.

There are two fundamental types of fin

rays, namely the true spinous rays and

soft rays that form the framework for fins.

Spinous rays are stiff and typically

unbranched, and they are located in a

single fin’s anterior part while soft rays

consist of longitudinal supports and are

typically branched. Even so, there are

exceptions. Some species like the

Silurichthys indragiriensis and Wallago

attu propel themselves forward or

backward by wavelike flexure of long

anal fins. Ichthyologists call these fins

“ribbon-fins” (Curet et al., 2011), and

what makes them so special is that the

entire stretch of the anal fin is actuated by

muscles along the body length. In eels, a

ribbon-fin may be present but the caudal

fin is almost absent and they rely mostly

on snake-like rectilinear locomotion for

swimming.

Most bony fishes have homocercal

caudal fins that can be forked, rounded,

truncated, and other symmetrical and non-

symmetrical forms (Fig. 12). Generally,

fishes with tapered body and fins are

67 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

proficient in high-speed propulsion in fast

flowing waters while fish with rounded

body and fins are associated with low-

speed movement in slow waters.

Mouth form and position also vary

greatly among fishes (Fig. 13). In most

fishes, the mouth is located terminally at

anterior tip of the head (e.g., Pristolepis

spp. and Oreochromis spp.), but in some

others it may be inferior (beneath the

snout, e.g., Pangio spp.) or superior

(upturned, e.g., Belodontichthys dinema)

depending on their feeding habits.

Generally, terminal mouths belong to

species that prefer to bite or seize their

prey while those with inferior mouths are

bottom feeders. Insectivorous fishes such

as the archer fish (Toxotes spp.) typically

have superior mouths and they feed on

insects that fall on the water surface.

Some freshwater species like the river

pipefish of the genus Doryichthys have a

tubular mouth to suck food from crevices.

Most fishes have protective scales

which vary greatly in size, structure,

squamation (scale coverage),

arrangement, sequence and colouration.

Scientifically, scales of teleost fishes can

be classified into the placoid, cosmoid,

elasmoid and ganoid categories (Sudo et

al., 2002). Teleost scales possess

outstanding hydrodynamic properties and

provide a resistant layer to protect fishes

from injury (Bruet et al., 2008). Scaled

skin is also known to play a critical role in

supporting fish locomotion by

synchronizing wave propagation (Long et

al., 1996), and by accumulating potential

energy like tendons (Hebrank and

Hebrank, 1986) for swimming efficiency.

As expected, scale counts are crucial for

fish identification (Fig. 14). Some genera

such as Clarias, Mystus and Ompok are

without scales, but they are no less

vulnerable. The skin of scaled and scale-

less fishes also secretes mucus to function

as a sealant or protection against

infection, and to reduce hydraulic friction

while swimming.

Evidently, some of the most interesting

features of fishes are their pigmentation

patterns (Fig. 15) which can be used as

critical references for taxonomic

identification purposes. Body colouration

is indeed an interesting subject in the

context of fish as a biological indicator.

Like all animals, fishes cannot synthesize

pigments. They have to ingest colourant

pigment like carotenoids from the food

they consume within their habitats, and

these can include fruits, insects and

phytoplankton (Grether, 2000). This can

reflect their foraging tendencies, habitat

health and especially the presence of

insect diversity as a rich source of

pigments. Many studies have shown that

fish mating behaviour is affected by

pigment availability from feeding habitats

and this, in turn, affects mate choice and

population abundance (Endler, 1980;

Basolo, 1990; Houde, 1997; Blount et al.,

2003).

Journal of Survey in Fisheries Sciences 4(1) 2017 68

Figure 12: Common caudal fin shapes (Source: Adapted from Rainboth, 1996).

Figure 13: Common mouth types.

Figure 14: Common meristic data collected by taxonomists (Source: Adapted from Rainboth, 1996

and Ambak, 2012).

69 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Figure 15: Common terms used to describe body markings and patterns on a representative

teleost.

Journal of Survey in Fisheries Sciences 4(1) 2017 70

The fundamental colour constituent in

fishes is the dermal chromatophore unit

(pigment cell) which consists of the: 1)

melanophore which contains melanin

(browns, blacks, and greys), 2)

xanthophore and erythrophore which

harbour carotenoids (yellows, orange and

red), and 3) iridophore, or sometimes

termed as iridocyte, which naturally

reflects external light source and provides

fishes their iridescence (Hawkes, 1974;

Fujii et al., 1989; Metz et al., 2006).

Chromatophores can naturally contract or

expand to induce or change colours to

blend into the aquatic environment for

camouflaging purposes. In some cases, a

combination of chromatophore units can

produce interesting colours. For example,

in the Siamese fighting fish (Betta

splendens), a wide variety of bodily

colours can be exhibited by the

permutation of iridophores,

melanophores, erythrophores and

xanthophores (Khoo et al., 2012; Khoo et

al., 2014).

It must be cautioned that identifying

species by their body colouration and

patterns alone is not entirely robust. In

certain cases, individuals in a natural

population may be affected by genetically

inherited conditions that cause them to

exhibit albinism, leucistic, melanistic and

xanthic abnormalities. Albino individuals

such as Silurus glanis, Astyanax

mexicanus, Hydrolagus colliei and

Genidens planifrons have been reported

(Dingerkus et al., 1991; Jeffery, 2006;

Reum et al., 2008; Leal et al, 2013) and

these individuals are unable to synthesize

tyrosine and melatonin hormones partially

or fully (Slavík et al., 2016). Individuals

affected by albinism are typically pale,

light pink, white or yellow (Lechner and

Ladich, 2010). Their eyes are generally

pink because blood is seen through the

colourless retina (Van Grouw, 2006).

Conversely, leucism is a condition

characterized by the reduction or absence

of most, if not all, of the pigment cell

types. Leucoptic individuals are generally

pale, white or yellow but they exhibit

normal retinal pigmentation (Quigley and

Wallace, 2013). Melanism is the exact

opposite of albinism where excessive

development of dark-coloured pigment

melanin occurs and the affected individual

is typically dark brown or black (Regan,

1961). It is a form of polymorphism that

is widespread in fishes, and it may be

genetically determined and/or influenced

by the environment (Price et al., 2006).

For example, melanin polymorphism has

been report in Gambusia holbrooki,

Siphateles bicolor mohavensis and

Amphilophus labiatus (Horth, 2002;

Henkanaththegedara and Stockwell, 2011;

Sowersby et al., 2014). When an

individual exhibits abnormal deep yellow,

orange or reddish pigmentation on the

body, this is attributed to excessive

development of the xanthophores and

erythrophores (Khoo et al., 2012).

Xanthic variety of the Cyprinus carpio

and Carasszus auratus with red, orange

and yellow pigmentation were first

reported and domesticated in China and

Japan as ornamental species (Kajishima,

1977; Balon, 1995). Wild individuals

from species such as Cyprinodon

bifasciatus have also been found to be

71 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

xanthic (Carson 2011). On the other hand,

an axanthic individual that lacks

xanthophores may be black, white, and/or

blue (Lewand et al., 2013). For example,

Parichy (2006) reported that axanthic

individuals have been found in species

from the Danio genus.

Being fully aquatic, fishes have vastly

different sensory systems compared to

those of terrestrial vertebrates. In fact,

they are endowed with more sensitive and

complex sensory organs to detect

vibration and sound. Fishes possess the

cephalic-lateralis system (Nelson, 1972)

that comprises a series of neuromast

sensory cells that run across the outer

layer of the head and body (Fig. 16).

Figure 16: An illustration of the fish cephalic-lateralis system consisting of neuromast sensors that

run across canals on the head and body (Source: Adapted from Nelson, 1972 and Iwata

and Jeon, 1995).

The neuromast contains fine hair cells

oriented in a manner to detect the

direction of vibration. Vibration signals

are then transmitted through special

canals and pits containing endolymphic

fluid to amplify the signals and thereafter

pass on to the brain. The location of the

lateralis system in fish can reflect their

feeding habits. Bottom feeders tend to

have the lateralis system on top of the

body to detect vibration from predators

that are lurking above. Those which feed

on the water surface normally have the

system along the ventral margin of the

body to track the presence of predators

below. Studies have also shown that the

lateralis system is responsible for obstacle

avoidance, triggering startle response and

schooling synchronization (Partridge and

Pitcher, 1979). The patterns and

configuration of cephalic-lateralis system

on fish bodies are sometimes used for fish

identification such as those from the

Kryptoglanis, Pseudorasbora and

Caecieleotri genus (Moncey, 2012;

Kawase and Hosoya, 2015; Walsh and

Chakrabarty, 2015).

In the case of cryptic species when the

species are too difficult to be

differentiated because they show small

external anatomical and morphological

deviations between species in the same

genus, ichthyologists have relied on the

internal organs to characterise them

(McCune, 1981). Where necessary, gill

rakers from the first gill arch on the left

Journal of Survey in Fisheries Sciences 4(1) 2017 72

side of the body are also counted for

meristic characterization such as species

from the Coregonus, Garra and Labeo

genus (Amundsen et al., 2004; Ayoade et

al., 2004; Krupp and Budd, 2009).

Correspondingly, in some species, the

pharyngeal teeth found on the fifth gill

arch are counted from left to right to assist

in meristic identification of species such

as those from the Moxostoma, Cycleptus,

Danio and Epalzeorhynchos genus

(Eastman 1977; Pasco-Viel et al., 2010).

All teleost fishes have an inner ear as

an auditory system. Instead of bony

ossicles, fishes have three pairs of

calcareous “ear stones”, or scientifically

termed as otoliths (Greek for “ear

stones”). The lapillus (“little stone” in

Latin) functions in maintaining body

balance and orientation, and the other

two, namely asteriscus (“little star” in

Latin) and sagittal (“arrow” in Latin),

peruse acoustic reception. Otoliths are

enclosed in a membranous sac together

with sensory hair cells or ciliary bundles.

Detection of mechanical signals will

occur when there are dynamic interactions

between otoliths and cilia (Assis, 2003;

Campana, 2005). Since Koken (1884)

reported that fish species can be

characterised by having otoliths of

different shapes and sizes, otolith

morphometry is fast becoming a trend to

identify fishes and some species such as

Netuma bilineata, Nuchequula nuchalis,

Coilia dussumieri and Garra rufa (Chen

et al., 2011; Thuy et al., 2015; Salimi et

al., 2016; Yedier et al., 2016). In 2006,

the AFORO online database was launched

(http://www.cmima.csic.es/aforo/) to

archive and share Fourier spectrum (FFT),

wavelet analysis (WT) and curvature scale

space analysis (CSS) data of otoliths

(Lombarte et al., 2006). At time of this

writing, the AFORO archive contains

4,672 high resolution images of 1,441

species from 221 families for reference.

Species Identification at the Molecular

Level

Morphological characterization is not

entirely robust. As mentioned earlier, the

concept of “species” is still subjected to

debate and not all taxonomists assign

meaningful categories to organisms by

morphotype. In many cases when

certainty cannot be attained, researchers

use terms like “subspecies”, “strain” or

“variant”. These are highly subjective and

confusing. In fish especially,

morphological plasticity between

individuals of the same species is

inherent. For example, body colour tones

and polymorphism exhibited by

individuals of the same species may vary

considerably depending on the diet

regime, habitat and season such as species

from the Betta, Poecilia and Danio genus

(Khoo et al., 1997; Price et al., 2008).

And this is where molecular analysis has

become a viable alternative.

Each organism is characterized by a

unique set of biological attributes that

enhance its fitness to survive in a niche

environment. Correspondingly, to adjust

to any changes in the environment, an

organism is naturally subjected to genetic

drift, mutation or variation

(polymorphism) as a mechanism to adapt.

Such natural phenomenon provides

73 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

markers at molecular level to detect

individual or species uniqueness (Sanger

et al., 1977). All molecular methods

depend on DNA marker or protein

sequence analysis and comparison to

determine molecular divergence over

evolutionary time based on the null

hypothesis of molecular evolution, or

better known as the “neutral theory”

(Kimura, 1968). Essentially, all methods

assume that individuals from the same

species have specific DNA (or protein)

sequences that vary, to a certain extent,

from individuals that belong to other

species. Nonetheless, the variance, or

“signature” of speciation (Sbordoni,

2010), is dependent on time and space and

subjected to biological productivity of

individuals, dispersal pattern and natural

genetic drift. Therefore, genetic

variability also occurs among individuals

of the same species. This means

establishing a credible locus, or the

position of a gene (Khoo et al., 2011)

from a phenotype is a prerequisite as

master reference for comparison purposes.

DNA markers can be classified in two

different types, namely type I which are

markers associated with genes with

known function and type II which are

markers are with anonymous genomic

segments (Chauhan and Rajiv, 2010). For

example, allozyme markers are classified

as type I protein markers and

microsatellites and other neutral markers

are considered type II (Hinsinger et al.,

2015). The DNA in all organisms is a

composition of four chemical bases –

adenine (A), guanine (G), cystosine (C),

and thymine (T) (Avise, 1994). Their

order or sequence in each gene is unique

to every species. Since Razin and Rottem

(1967) have successfully employed

protein analysis for characterising

microorganism species, modern advances

have adapted the concept of analysing A-

G-C-T bases in various DNA genetic

markers. In fish identification, the

common DNA analyses applied are length

polymorphism (RFLP), amplified

fragment length polymorphism (AFLP),

random amplified polymorphic DNA

(RAPD), microsatellites or simple

sequence repeat (SSR), single nucleotide

polymorphism (SNP) and expressed

sequence tag (EST) markers (O’Reilly

and Wright, 1995; Khoo et al., 2003;

Sampaio et al., 2003; Teletchea, 2009;

Chauhan and Rajiv, 2010; Khoo et al.,

2011; Kress et al., 2015).

Fish genome typically contains

roughly a billion nucleotide pairs (Stepien

and Kocher, 1997), and analysing all of

them would be too daunting and the

results would cause an information

overload. Since Herbert et al. (2003)

discovered a technique to amplify the

mitochondrial cytochrome c oxidase

subunit 1 (COI) gene. There is now a

consensus to analyse a 648-base pair (bp)

region of COI to rapidly identify a fish

species (Cawthorn et al., 2012). Such an

approach is now known as DNA

barcoding and it has gained widespread

acceptance as a fast, cost effective and

standardised technique. So far, the Fish

Barcode of Life Initiative has barcoded

7,882 fish species, which is only

approximately 25% of the estimated

Journal of Survey in Fisheries Sciences 4(1) 2017 74

31,220 species present globally (Jinbo et

al., 2011).

It should be stressed that identified

species through DNA barcode is only as

good as the voucher specimen's DNA

barcode made available and archived in

platform such as GenBank. Hence, if a

DNA barcode is inaccurate or

compromised due to issues such as

carryover DNA contamination,

incomplete genotyping of loci throughout

the genome, low/wrong quality DNA

material, human errors, biases and some

other critical risks (Bridge et al., 2003;

Forster, 2003; Moritz and Cicero,

2004; Smith and Burgoyne, 2004; Ebach

and Holdrege, 2005; Meyer and Paulay,

2005; Will et al., 2005), the identification

process would be erroneous. Ross et al.

(2008) proposed that reference sequences

of at least five or more voucher specimens

from various geographical sites should be

acquired. Unfortunately, this also means

that DNA analysis is not a one minute

procedure. To conduct it properly, the

process of acquiring exemplar genotypes

is tedious and costly because some

species are found in large regions and

various countries.

In the recent years, DNA sequencing

techniques have made substantial progress

and they are able to analyse 30 to 1,500

nucleotides (nt) for hundreds of thousands

to millions of DNA molecules in a single

process within a complex or degraded

DNA source (Davey and Blaxter, 2011;

Mehinto et al., 2012). These are classified

as next-generation sequencing (NGS)

technologies (Tillmar et al., 2013) and

sometimes termed as "DNA

metabarcoding" to refer to their ability to

automatically identify multiple species

from a single bulk sample (Taberlet et al.,

2012). Because NGS technologies can

extract massive numbers of reads, the

results increase the chances of finding and

annotating matches (Hemmer-Hansen et

al., 2014). So far, technological platforms

that are able to produce and analyse

gigabases of DNA sequence include

Illumina, Roche, AB SOLiD, 454 GS

FLX, Ion Torrent, HeliScope, Starlight

and PacBio (Rothberg and Leamon, 2008;

Pandey et al., 2008; Davey and Blaxter,

2011; Hemmer-Hansen et al., 2014). They

differ from each other based on amount of

sequence information generation,

chemistry protocol for sequencing and the

length of sequence read (Mehinto et al.,

2012).

Reference Type and Traceability

The hallmark of the taxonomy discipline

is its persistency in collecting, preserving

and managing specimens as essential

physical references for species-level

research. Although ecologists,

conservationists, aquaculturists or

researchers who adopt fish as a part of

their studies need not master the specifics

in specimen management, it is useful to

briefly understand the ICZN zoological

code and terms as a precaution against

negligence when tracing the correct

binomial nomenclature and description of

fish.

Fundamentally, in taxonomy,

a “type” is a specimen of a distinct

species which is used as master reference

(Krell and Wheeler, 2014). Each species

75 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

or subspecies that is scientifically named

by the original author (discoverer) is

traceable to a name-bearing specimen

which was first found and kept in a

particular museum. A new species cannot

be described and registered formally

without depositing a single physical

whole fish known as a “holotype” in the

museum (Clemann et al., 2014; Kumar

and Hassan, 2015). As sexual dimorphism

occurs in many fish species, it is good

practice to deposit an opposite sex

specimen of the holotype and it is

assigned as an “allotype” (Jorge et al.,

2014). Also, polymorphisms may occur in

certain fishes and a holotype is not

expected to be a typical representative

(Hulsey, 2005), although in an ideal case

it should be. To mitigate this,

morphotypes that show morphological

variants of a species can be established,

and molecular analysis is usually carried

out to determine whether the variations

are due to polymorphism or if it is a new

species (Simonov, 2008).

A researcher may also designate a

duplicate specimen of the holotype and

such a specimen is termed as an

“isotype”. When a better specimen is

eventually deposited, the holotype is not

superseded. According to the ICZN code,

such a specimen which provides better

clarity is known as an “epitype” and it

may be deposited when the holotype is

evidently imprecise. In the case when a

holotype is lost or damaged, a “neotype”

specimen may also be deposited as

replacement. While there can only be one

holotype, taxonomists can continue to

deposit specimens in any museums

around the world for the type series (a

range of specimens showing variation in

the species). These comparable specimens

are termed as “paratypes” and they have

no name-bearing role.

In situations when the researcher fails

to establish a holotype, the existing two or

more specimens collected and deposited

in the museums can be used to describe

and name a species. These deposited

specimens are known as “syntypes”

although such practice is now rarely used

in contemporary taxonomy. A master

reference specimen selected from

syntypes is termed as “lectotype” and

when a lectotype is finally established, all

other syntypes shall be, by default,

reassigned as “paralectotypes”.

Correspondingly, any duplicate specimen

of the lectotype is called an

“isolectotype”. Finally, specimens that

have been erroneously described, named

or labelled are annotated as “non-types”.

All terminologies pertaining to types

mentioned in this section are elaborated in

detail by ICZN at the website

http://www.iczn.org/iczn/index.jsp.

The responsibility rests on the

taxonomist to maintain the specimens and

make them accessible for current and

future studies (Krell and Wheeler, 2014;

Rocha et al., 2014). To consolidate a large

quantity of voucher specimen database in

a museum, the taxonomist is also

expected to occasionally publish

monographs that contain summarised

information of all species in a group to

update the scientific community (Grinnell,

1910; Pyke et al., 2010; Kottelat, 2013).

Journal of Survey in Fisheries Sciences 4(1) 2017 76

In the advent of technological

advancement, non-destructive methods

such as high-resolution photography,

computerised tomography (CT) scan and

radiography methods that can record the

physical characteristics of specimens, the

work of a taxonomist has expanded over

the years. There are already attempts to

digitalize specimens using these

technologies. For example, Berquist et al.

(2012) have progressively scanned

specimens with the magnetic resonance

imaging (MRI) technology and created an

online digital archive called Digital Fish

Library (DFL,

http://www.digitalfishlibrary.org) to share

high-resolution and high-contrast visual

data. The Biovisualization Center at the

University of Washington has also just

initiated a program that applies the CT

scanning technology and the captured 3D

morphology data of fish specimens is

shared through the Open Science

Framework website

(https://osf.io/ecmz4/wiki/Fishes/). Such

innovations have the potential to replace

pale and degraded voucher specimens that

have been preserved for a long period of

time in alcohol. Morphological and

meristic database compilation can be

instantly peer-reviewed and shared online

with any amateurs or experts located

anywhere around the world. This is an

opportunity for scientists to engage more

with the society and garner support from

the public and policymakers for fish

conservation.

Specimen Collection and Preservation

In principle, a scientific finding must be

reproducible. When an author declares

and publishes the description of a new

species, a specimen (i.e., haplotype) must

be deposited permanently in the museum

so that the author's claim can be critically

appraised and reappraised by others

(Rocha et al., 2014). The specimen can be

refuted or disputed by other ichthyologists

to allow for revisions. Similarly, when a

researcher conducts a fish inventory

investigation that results in a scientific or

journal report, it is a good practice

(although not compulsory) to collect

voucher specimens for future verification

and to promote transparency. This

approach also provides physical records

that allow researchers to scrutinize the

inter- and intraspecific variation of

species collected at different periods of

time and localities.

Specimens are typically acquired by

various capturing methods as discussed

widely elsewhere by literature such as by

handnets, traps, seine nets, electrofishing

and even by buying directly from

fishermen or the local fresh markets. Once

obtained, they must be immediately

labelled with 1) serial number, 2) species

name, 3) name of collector, 4) location, 5)

date of collection, 6) GPS coordinates,

and 7) some description of the specimens’

colour and body markings in fresh should

be recorded (Fischer, 2013; Motomura

and Ishikawa, 2013). This may be

supported by high resolution photographs

of the whole fish and specific parts with

distinctive characters (Figs. 17, 18 and

19).

77 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Figure 17: Fresh specimen is photographed facing left together with a ruler to indicate scale.

Figure 18: A live specimen is best photographed with high-resolution photography to record subtle

details and colouration.

Figure 19: Noticeable variations of the same species should be photographed for species-level

studies. For example, in the case of Tor tambra (above), individuals in the same

population may display differing forms of mental lobe and barbels (Roberts, 1999).

Journal of Survey in Fisheries Sciences 4(1) 2017 78

Specimens should be cleaned and can

either be frozen or immediately fixed in

formalin or alcohol before being

transferred to depositories.

In fish taxonomy, the left side of the

fish body is examined. Therefore if

muscle tissue is required for molecular

analysis, it should be dissected from the

right side of the body. In small fishes

where muscle tissues are difficult to

excise, the right pelvic fin may be

collected as an alternative (Shiozawa et

al., 1992). Typically, 1.0 cm3 tissue from

the fresh muscle contains enough genomic

material for molecular study and it should

be stored in 95% alcohol and then

refrigerated at -20°C (Motomura and

Ishikawa, 2013). Preferably, it should be

free from fat and blood which may

hamper the DNA purification process

(Wong et al., 2012). Chakraborty et al.

(2006) suggest that in the absence of

refrigeration during field work, specimens

fixed in 10% buffered formalin or 95%

alcohol should be analyzed with DNA

processes within one week to produce the

best results.

In the museums and depositories,

taxonomists are cautious when fixing and

storing specimens (Fig. 20) since any flaw

in the process will devalue their academic

significance. Specimens are usually fixed

in 10% formalin solution and large sized

specimens are incised on the right side to

enable better absorption of formalin

(Schander and Halanych, 2003; Garrigos

et al., 2013). For the same purpose,

formalin may also be injected into the

abdomen by using a syringe (Motomura

and Ishikawa, 2013).

Figure 20: Fixed specimens are usually stored in glass jars with heads pointing downwards. Note

that specimens become pale and lose their colouration quality, which is why

photography of live specimens is crucial as part of the data collection process.

79 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Taxonomic Key

After fixing, labelling and cataloguing a

specimen, a competent taxonomist would

carry out the standard morphometrics,

meristics and sometimes molecular

analyses as mentioned earlier. As a

minimum, the taxonomist would

subsequently generate a report with the

following information (Fischer, 2013) for

each species;

1. Species name, author and year.

2. Material examined – description of type

material and voucher specimen

examined.

3. Diagnosis – description of the

specimen’s key markers or

morphological features that

differentiates it from nearest congeners

from the same watershed and other

watersheds. Diagrams may be included

for clarity.

4. Description – description of major

morphological and meristic data.

5. Pigmentation in life – description of

colour, marking and patterns on the

body and fins of a fresh specimen.

6. Colour in formalin or alcohol –

description of colour, markings and

patterns on the body and fins of the

fixed specimen.

7. Distribution – description of location

where the specimen and the species

can be typically found according to

published literature.

8. Etymology – description of the

Greek/Latin word or rationale behind

the scientific name (binomial

nomenclature) assigned to the species.

9. Field notes – description of sympatric

and syntonic species found in the same

habitat when the specimen is collected.

10. Remarks or comments – description of

precautions as a measure against

misidentification and any other useful

information for effective identification.

If a potential new species is

encountered, the specimen and full-

colour photographs are to be sent to an

authority of the genus for further

investigation. This shall be recorded in

this section.

A competent taxonomist would update

the field “taxonomic key” for the

corresponding genus once a new species

has been identified. It is a conventional

tool meant for quick and practical

identification based on the major

morphological characters (Fig. 21) of a

species (Fischer, 2013). A typical

taxonomic key is organized in a series

diagnostic characteristic of a species that

lead the user to the correct name of a

given specimen. A taxonomic key is

called a dichotomous key (in Latin

“dichotomous” means in two parts)

because only two marker options are

offered in each step (Fig. 22). The

markers provided may be quantitative

(e.g., scale count) or qualitative (e.g.,

body colour). Once created, the key can

be continuously improved by taxonomists

based on feedback from users.

Journal of Survey in Fisheries Sciences 4(1) 2017 80

Figure 21: The key characteristics of a genus are typically described at the start of the taxonomic

key. For example, the Glyptothorax genus’s key characteristic is the presence of a

unique thoracic adhesive apparatus (arrow) that can only be observed in the ventral

view.

Figure 22: An example of a dichotomous key produced by Silfvergrip (2009, p.25) for the

identification of freshwater eels from the Anguillidae family.

81 Keat-Chuan Ng et al., A Review of Fish Taxonomy Conventions and Species Identification …

Integrative taxonomy

There are species within the same genus

that possess small variations that are not

easy to discriminate. This is compounded

by the unstable and convoluted taxonomic

history of some species which can

experience numerous revisions of species

names because taxonomists may not share

the same assumptions and approaches.

Correspondingly, it is fair to expect that

the science of taxonomy and systematics

is constantly in flux and revisions may be

frequent.

A classic example is the case of

Neolissochilus spp. and Tor spp. found in

Southeast Asia. These genera are typically

prone to trophic polymorphism and

display conspicuous oral morphology

variation (Roberts and Khaironizam,

2008) that have confused even the most

experienced ichthyologists. For example,

in early 20th Century, members of the

Neolissochilus genus were placed in the

Barbus genus (Boulenger, 1893; Duncker,

1904). Later they were reassigned

respectively to Labeobarbus,

Crossochilus, Puntius and Acrossocheilus

(Weber and de Beaufort 1916; Ahl 1933;

Fowler 1934; Herre and Myers 1937;

Smith 1945) before being finalized as

Neolissochilus, a new genus created by

Rainboth (1996).

In cases when the taxonomy of a

particular genus has stabilized,

misidentification can still be common

because small variations can be difficult

to be distinguished. For example, in the

past decades, there were numerous reports

that highlighted misidentification of the

freshwater eels from the Anguillidae

family due to species and subspecies from

the family have sympatric distribution and

the morphological characters among them

are hard to distinguish (Castle and

Williamson, 1974; Aoyama et al., 2000;

Arai and Wong 2016). For example,

Sugeha and Suharti (2009) found

difficulty in distinguishing Anguilla

bicolor bicolor and Anguilla bicolor

pacifica based on morphological

attributes alone. However, they were able

to make a distinction between the species

by their adult sizes. Generally, A. bicolor

bicolor is longer and heavier than A.

bicolor pacifica. They also found that A.

bicolor bicolor tend to occur in Sumatra

and Java region and A. bicolor pacifica is

found in Sulawasi and New Guinea region

of Indonesia. As such, they have proposed

that the two subspecies can be

distinguished by the geographic approach.

Subsequently, Teng et al. (2009) resolved

the issue by conducting a phylogenic

study and validated the notion that

Anguilla species and subspecies can

cluster regionally (Fig. 23).

The case of Anguilla genus is a classic

example how the combination of

morphological and molecular approaches,

generally termed as integrative taxonomy

(Goulding and Dayrat, 2016), are crucial

in gaining and expanding the

understanding of taxonomy and diversity

in fish. This demonstrates that the

broadest range of methods should be

utilized to answer and solve taxonomic

concerns.

Journal of Survey in Fisheries Sciences 4(1) 2017 82

Figure 23: The morphological phylogenetic tree of the genus Anguilla showing correlation species

occurrence in various regions (Source: Teng et al., 2009).

Acknowledgements

We wish to extend our deepest gratitude

to all past and present taxonomists around

the world whose life time work and

publications have provided substance for

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